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I used bwa mem to align the DNA with the reference genome. If there are split reads (chimeric reads, come from two different parts of the genome), will it be split into two lines rather than one line?

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    $\begingroup$ Split reads as in spliced or split reads as in a read with a supplemental alignment? "Split reads" has many possible meanings. $\endgroup$
    – Devon Ryan
    Jun 16, 2022 at 8:18
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    $\begingroup$ Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking. $\endgroup$
    – Community Bot
    Jun 16, 2022 at 12:58
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    $\begingroup$ split reads here refer to chimeric reads which come from two different parts of the genome. For example, the first 1-70 bp is from a region in chromosome 1, 71-150bp is from a region in chromosome 3. $\endgroup$
    – Wang Ming
    Jun 19, 2022 at 5:49

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I'm assuming you mean supplementary/chimeric alignment? The SAM Format Specification has a really detailed explanation as well as its Optional Fields Specification.

In general though, you will have an additional line in the SAM file to represent a chimeric alignment yes. For a single read, one line will represent the primary alignment; this is arbitrarily chosen. The other line will represent the split/supplementary alignment and have its supplementary alignment flag set. If there are multiple chimeric alignments, each one will have its own line.

You check if a primary alignment has any supplementary alignments associated to it by checking the SA tag which will list the location(s) of any supplementary alignment(s).

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